#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 100000 100000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 100 1 100 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00064 0.111135 8304 2 97.7007 9.09306 2768 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.25 | 17.15 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 -3703.1158 140505.98 1.42352 406.71708 6.44486 23.132256 0 0 36207.244 -66975.859 -315.99625 -291763.89 -322502.93 9247.778 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.2369e-06 8304 2 103.7 0.000103161 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.47488e-06 8304 2 103.7 9.69789e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32026e-06 8304 2 103.7 9.62263e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.0618e-06 8304 2 103.7 9.6414e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.23514e-06 8304 2 103.7 0.000102009 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.42156e-06 8304 2 103.7 0.000111205 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.44402e-06 8304 2 103.7 9.72153e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.11292e-06 8304 2 103.7 9.98743e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.24838e-06 8304 2 103.7 9.19654e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.48285e-06 8304 2 103.7 0.000105646 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.42978e-06 8304 2 103.7 0.000100523 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.42071e-06 8304 2 103.7 0.000100763 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.21016e-06 8304 2 103.7 9.9793e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 2.44559e-06 8304 2 103.7 0.000131632 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.35658e-06 8304 2 103.7 0.000106595 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.23191e-06 8304 2 103.7 0.000118928 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.29619e-06 8304 2 103.7 0.000101944 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.0324e-06 8304 2 103.7 9.38741e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.38765e-06 8304 2 103.7 9.64226e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.04201e-06 8304 2 103.7 8.80724e-05 2768 1000000 1000000 -234.18056 140505.98 1.42352 299.70713 41.848576 69.21725 0 0 34444.48 -50954.883 -315.99625 -291936.32 -308335.66 6814.6266 Loop time of 23728.3 on 8 procs for 1000000 steps with 10721 atoms Performance: 3.641 ns/day, 6.591 hours/ns, 42.144 timesteps/s 98.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4092.8 | 14213 | 18803 |4887.9 | 59.90 Bond | 1.18 | 5.1471 | 8.6394 | 115.0 | 0.02 Kspace | 3163.5 | 7757.8 | 17887 |6622.7 | 32.69 Neigh | 989.27 | 990.41 | 991.83 | 3.1 | 4.17 Comm | 250.37 | 281.12 | 300.64 | 109.2 | 1.18 Output | 0.024935 | 0.028026 | 0.030921 | 1.2 | 0.00 Modify | 436.27 | 451.34 | 471.35 | 59.8 | 1.90 Other | | 29.45 | | | 0.12 Nlocal: 1340.12 ave 1602 max 714 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11117.9 ave 13220 max 9554 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 626336 ave 807888 max 177016 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5010689 Ave neighs/atom = 467.37142 Ave special neighs/atom = 1.6069397 Neighbor list builds = 49606 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.04201e-06 8304 2 103.7 8.80724e-05 2768 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.28 | 17.25 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 1000000 1000000 -233.59105 140505.98 1.42352 299.70713 41.848576 69.21725 0 0 34444.48 -50954.883 -315.99625 -291936.32 -308335.66 6814.6266 Loop time of 3.45075e-06 on 8 procs for 0 steps with 10721 atoms 126.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.451e-06 | | |100.00 Nlocal: 1340.12 ave 1602 max 714 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11117.9 ave 13220 max 9554 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 626336 ave 807888 max 177016 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5010689 Ave neighs/atom = 467.37142 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out